This gene encodes a member of the DEAD box protein family. DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), are putative RNA helicases. They are implicated in a number of cellular processes involving alteration of RNA secondary structure, such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. Bas... See more...

Aliases for DDX23 Gene

Aliases for DDX23 Gene

  • DEAD-Box Helicase 23 2 3 5
  • DEAD (Asp-Glu-Ala-Asp) Box Polypeptide 23 2 3
  • Probable ATP-Dependent RNA Helicase DDX23 3 4
  • 100 KDa U5 SnRNP-Specific Protein 3 4
  • PRP28 Homolog, Yeast 2 3
  • DEAD Box Protein 23 3 4
  • SNRNP100 2 3
  • U5-100K 2 3
  • PRPF28 2 3
  • Prp28 2 3
  • U5 SnRNP 100 KD Protein 3
  • PRP28p Homolog 3
  • PRP28 Homolog 4
  • EC 3.6.4.13 4
  • U5-100KD 3
  • U5-100kD 4
  • EC 3.6.1 51
  • DDX23 5

External Ids for DDX23 Gene

Previous GeneCards Identifiers for DDX23 Gene

  • GC12M048940
  • GC12M047509
  • GC12M049223
  • GC12M046256

Summaries for DDX23 Gene

Entrez Gene Summary for DDX23 Gene

  • This gene encodes a member of the DEAD box protein family. DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), are putative RNA helicases. They are implicated in a number of cellular processes involving alteration of RNA secondary structure, such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. Based on their distribution patterns, some members of this family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. The protein encoded by this gene is a component of the U5 snRNP complex; it may facilitate conformational changes in the spliceosome during nuclear pre-mRNA splicing. An alternatively spliced transcript variant has been found for this gene, but its biological validity has not been determined. [provided by RefSeq, Jul 2008]

GeneCards Summary for DDX23 Gene

DDX23 (DEAD-Box Helicase 23) is a Protein Coding gene. Diseases associated with DDX23 include Distal Hereditary Motor Neuronopathy Type 2 and Spinal Muscular Atrophy, Type I. Among its related pathways are mRNA Splicing - Minor Pathway and Gene Expression. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and ATP-dependent RNA helicase activity. An important paralog of this gene is DDX46.

UniProtKB/Swiss-Prot Summary for DDX23 Gene

  • Involved in pre-mRNA splicing and its phosphorylated form (by SRPK2) is required for spliceosomal B complex formation (PubMed:18425142). Independently of its spliceosome formation function, required for the suppression of incorrect R-loops formed during transcription; R-loops are composed of a DNA:RNA hybrid and the associated non-template single-stranded DNA (PubMed:28076779).

Gene Wiki entry for DDX23 Gene

Additional gene information for DDX23 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for DDX23 Gene

Genomics for DDX23 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for DDX23 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around DDX23 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for DDX23

Top Transcription factor binding sites by QIAGEN in the DDX23 gene promoter:
  • CBF(2)
  • CBF-A
  • CBF-B
  • CP1A
  • Egr-4
  • NF-Y
  • NF-YA
  • NF-YB
  • POU2F1
  • POU2F1c

Genomic Locations for DDX23 Gene

Genomic Locations for DDX23 Gene
chr12:48,829,756-48,852,842
(GRCh38/hg38)
Size:
23,087 bases
Orientation:
Minus strand
chr12:49,223,539-49,246,625
(GRCh37/hg19)
Size:
23,087 bases
Orientation:
Minus strand

Genomic View for DDX23 Gene

Genes around DDX23 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
DDX23 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for DDX23 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for DDX23 Gene

Proteins for DDX23 Gene

  • Protein details for DDX23 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BUQ8-DDX23_HUMAN
    Recommended name:
    Probable ATP-dependent RNA helicase DDX23
    Protein Accession:
    Q9BUQ8
    Secondary Accessions:
    • B2R600
    • B4DH15
    • O43188

    Protein attributes for DDX23 Gene

    Size:
    820 amino acids
    Molecular mass:
    95583 Da
    Quaternary structure:
    • The phosphorylated form (by SRPK2) is a component of the U4/U6-U5 tri-snRNP complex composed of the U4, U6 and U5 snRNAs and at least PRPF3, PRPF4, PRPF6, PRPF8, PRPF31, SNRNP200, TXNL4A, WDR57, SNRNP40, DDX23, CD2BP2, PPIH, SNU13, EFTUD2, SART1 and USP39 (PubMed:16723661, PubMed:9409622). Identified in the spliceosome C complex (PubMed:11991638). Interacts with ERBB4 (PubMed:20858735). Interacts with ERCC6 (PubMed:26030138).

    Three dimensional structures from OCA and Proteopedia for DDX23 Gene

    Alternative splice isoforms for DDX23 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for DDX23 Gene

Selected DME Specific Peptides for DDX23 Gene

Q9BUQ8:
  • PTRELAQQ
  • VLDEADRM
  • VSMVVNYD
  • AETGSGKT
  • HRIGRTGR
  • VIATPGR
  • DEADRMID
  • GVAITFL
  • LAPTREL
  • TGSGKTAAF
  • TPGRLID
  • GRTGRAG
  • APTRELA
  • IATPGRL
  • YIHRIGR

Post-translational modifications for DDX23 Gene

  • In vitro phosphorylated by CLK1 and U1 snRNP-associated protein kinase (PubMed:9409622). Phosphorylated by SRPK2 and this phosphorylation is required for its association with the tri-snRNP (U4/U6-U5 tri-small nuclear ribonucleoproteins) and subsequent spliceosomal B complex formation (PubMed:18425142). May be phosphorylated by SRPK2 on Ser residues in the SR domain; the phosphorylation is required for the removal of inappropriate R-loops during transcription (PubMed:28076779).
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for DDX23 Gene

Domains & Families for DDX23 Gene

Gene Families for DDX23 Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Protein Domains for DDX23 Gene

Suggested Antigen Peptide Sequences for DDX23 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ54028, highly similar to Probable ATP-dependent RNA helicase DDX23 (EC 3.6.1.-) (B4DH15_HUMAN)
  • U5-100kD (DDX23_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9BUQ8

UniProtKB/Swiss-Prot:

DDX23_HUMAN :
  • Belongs to the DEAD box helicase family. DDX23/PRP28 subfamily.
Family:
  • Belongs to the DEAD box helicase family. DDX23/PRP28 subfamily.
genes like me logo Genes that share domains with DDX23: view

Function for DDX23 Gene

Molecular function for DDX23 Gene

UniProtKB/Swiss-Prot Function:
Involved in pre-mRNA splicing and its phosphorylated form (by SRPK2) is required for spliceosomal B complex formation (PubMed:18425142). Independently of its spliceosome formation function, required for the suppression of incorrect R-loops formed during transcription; R-loops are composed of a DNA:RNA hybrid and the associated non-template single-stranded DNA (PubMed:28076779).
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=ATP + H2O = ADP + H(+) + phosphate; Xref=Rhea:RHEA:13065, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616, ChEBI:CHEBI:43474, ChEBI:CHEBI:456216; EC=3.6.4.13;.

Enzyme Numbers (IUBMB) for DDX23 Gene

Phenotypes From GWAS Catalog for DDX23 Gene

Gene Ontology (GO) - Molecular Function for DDX23 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000166 nucleotide binding IEA --
GO:0003676 nucleic acid binding IEA --
GO:0003723 RNA binding IBA 21873635
GO:0003724 RNA helicase activity TAS 9409622
GO:0004386 NOT helicase activity IDA 9539711
genes like me logo Genes that share ontologies with DDX23: view
genes like me logo Genes that share phenotypes with DDX23: view

Animal Model Products

  • Taconic Biosciences Mouse Models for DDX23

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for DDX23

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for DDX23 Gene

Localization for DDX23 Gene

Subcellular locations from UniProtKB/Swiss-Prot for DDX23 Gene

Nucleus. Chromosome. Note=During transcription, accumulates at chromatin loci where unscheduled R-loops form and colocalizes with paused 'Ser-5'-phosphorlyated POLR2A/RNA polymerase II and kinase SRPK2. {ECO:0000269 PubMed:28076779}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for DDX23 gene
Compartment Confidence
nucleus 5
extracellular 4
plasma membrane 2
mitochondrion 2
cytoskeleton 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (3)
  • Nucleoplasm (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for DDX23 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000785 chromatin IDA 28076779
GO:0005634 nucleus TAS,IDA 28076779
GO:0005654 nucleoplasm TAS --
GO:0005681 spliceosomal complex IEA --
GO:0005682 U5 snRNP IDA 9539711
genes like me logo Genes that share ontologies with DDX23: view

Pathways & Interactions for DDX23 Gene

genes like me logo Genes that share pathways with DDX23: view

Pathways by source for DDX23 Gene

Gene Ontology (GO) - Biological Process for DDX23 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000354 cis assembly of pre-catalytic spliceosome IC 9539711
GO:0000375 RNA splicing, via transesterification reactions TAS 9409622
GO:0000398 mRNA splicing, via spliceosome TAS --
GO:0006397 mRNA processing IEA --
GO:0008380 RNA splicing TAS 9409622
genes like me logo Genes that share ontologies with DDX23: view

No data available for SIGNOR curated interactions for DDX23 Gene

Drugs & Compounds for DDX23 Gene

(3) Drugs for DDX23 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Phosphoric acid Approved Pharma 0
Water Approved Pharma 0
ATP Investigational Nutra Agonist, Activator, Partial agonist, Antagonist, Full agonist, Gating inhibitor, Pore Blocker, Potentiation 0

(1) Additional Compounds for DDX23 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
ADP
  • 5'-Adenylphosphoric acid
  • Adenosine 5'-diphosphate
  • ADENOSINE-5'-diphosphATE
  • H3ADP
  • 5'-Adenylphosphate
Agonist, Full agonist, Partial agonist, Gating inhibitor, Antagonist 58-64-0
genes like me logo Genes that share compounds with DDX23: view

Transcripts for DDX23 Gene

mRNA/cDNA for DDX23 Gene

1 REFSEQ mRNAs :
7 NCBI additional mRNA sequence :
18 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for DDX23

Alternative Splicing Database (ASD) splice patterns (SP) for DDX23 Gene

ExUns: 1 ^ 2a · 2b · 2c ^ 3 ^ 4 ^ 5a · 5b ^ 6a · 6b · 6c ^ 7a · 7b ^ 8 ^ 9a · 9b · 9c ^ 10a · 10b ^ 11a · 11b ^ 12 ^ 13a · 13b ^ 14 ^ 15 ^
SP1: - - - -
SP2: - - - - - -
SP3: - - - - -
SP4: - - - - - -
SP5: -
SP6: - -
SP7: - - -
SP8:
SP9: -
SP10: -
SP11:
SP12:
SP13:

ExUns: 16 ^ 17a · 17b ^ 18a · 18b ^ 19a · 19b ^ 20a · 20b ^ 21a · 21b
SP1: - -
SP2: - -
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12: -
SP13: -

Relevant External Links for DDX23 Gene

GeneLoc Exon Structure for
DDX23

Expression for DDX23 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for DDX23 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for DDX23 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (14.1) and CD8 Tcells (8.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for DDX23 Gene



Protein tissue co-expression partners for DDX23 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for DDX23

SOURCE GeneReport for Unigene cluster for DDX23 Gene:

Hs.130098

Evidence on tissue expression from TISSUES for DDX23 Gene

  • Nervous system(5)
  • Lung(4.7)
  • Skin(2.6)
  • Intestine(2.5)
  • Pancreas(2)
genes like me logo Genes that share expression patterns with DDX23: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for DDX23 Gene

Orthologs for DDX23 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for DDX23 Gene

Organism Taxonomy Gene Similarity Type Details
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 100 (a)
OneToMany
-- 31
  • 99 (a)
OneToMany
-- 31
  • 91 (a)
OneToMany
-- 31
  • 87 (a)
OneToMany
Chimpanzee
(Pan troglodytes)
Mammalia DDX23 30 31
  • 99.63 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia DDX23 31
  • 98 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia DDX23 30 31
  • 94.02 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia DDX23 30 31
  • 92.97 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Ddx23 30 17 31
  • 90.96 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Ddx23 30
  • 90.92 (n)
Chicken
(Gallus gallus)
Aves -- 31
  • 98 (a)
OneToMany
-- 31
  • 98 (a)
OneToMany
DDX23 30
  • 82.49 (n)
Lizard
(Anolis carolinensis)
Reptilia DDX23 31
  • 91 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.24773 30
Zebrafish
(Danio rerio)
Actinopterygii ddx23 30 31
  • 77.13 (n)
OneToOne
wufi39b12 30
Fruit Fly
(Drosophila melanogaster)
Insecta CG10333 30 31
  • 64.86 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007825 30
  • 54.6 (n)
Worm
(Caenorhabditis elegans)
Secernentea ddx-23 30 31
  • 62.75 (n)
OneToOne
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PRP28 31 33
  • 38 (a)
OneToMany
Thale Cress
(Arabidopsis thaliana)
eudicotyledons AT2G33730 30
  • 57.38 (n)
Soybean
(Glycine max)
eudicotyledons Gma.3548 30
Rice
(Oryza sativa)
Liliopsida Os03g0708600 30
  • 57.69 (n)
Os.3228 30
Barley
(Hordeum vulgare)
Liliopsida Hv.2391 30
Wheat
(Triticum aestivum)
Liliopsida Ta.3307 30
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 68 (a)
OneToOne
Bread mold
(Neurospora crassa)
Ascomycetes NCU02803 30
  • 57.78 (n)
Fission Yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes prp28 30
  • 53.22 (n)
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.11344 30
Species where no ortholog for DDX23 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Tropical Clawed Frog (Silurana tropicalis)

Evolution for DDX23 Gene

ENSEMBL:
Gene Tree for DDX23 (if available)
TreeFam:
Gene Tree for DDX23 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for DDX23: view image

Paralogs for DDX23 Gene

(11) SIMAP similar genes for DDX23 Gene using alignment to 6 proteins:

  • DDX23_HUMAN
  • B4DH15_HUMAN
  • F8VVA2_HUMAN
  • F8W1J5_HUMAN
  • H0YI52_HUMAN
  • H0YIL9_HUMAN

Pseudogenes.org Pseudogenes for DDX23 Gene

genes like me logo Genes that share paralogs with DDX23: view

Variants for DDX23 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for DDX23 Gene

SNP ID Clinical significance and condition Chr 12 pos Variation AA Info Type
732990 Benign: not provided 48,836,716(-) A/G SYNONYMOUS_VARIANT
862674 Uncertain Significance: not provided 48,830,668(-) G/A MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for DDX23 Gene

Structural Variations from Database of Genomic Variants (DGV) for DDX23 Gene

Variant ID Type Subtype PubMed ID
nsv826363 CNV gain 20364138
nsv976609 CNV duplication 23825009

Variation tolerance for DDX23 Gene

Residual Variation Intolerance Score: 2.91% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.57; 12.25% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for DDX23 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
DDX23

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for DDX23 Gene

Disorders for DDX23 Gene

MalaCards: The human disease database

(2) MalaCards diseases for DDX23 Gene - From: DISEASES

- elite association - COSMIC cancer census association via MalaCards
Search DDX23 in MalaCards View complete list of genes associated with diseases
genes like me logo Genes that share disorders with DDX23: view

No data available for UniProtKB/Swiss-Prot and Genatlas for DDX23 Gene

Publications for DDX23 Gene

  1. The human U5 snRNP-specific 100-kD protein is an RS domain-containing, putative RNA helicase with significant homology to the yeast splicing factor Prp28p. (PMID: 9409622) Teigelkamp S … Lührmann R (RNA (New York, N.Y.) 1997) 2 3 4 23
  2. Phosphorylation of human PRP28 by SRPK2 is required for integration of the U4/U6-U5 tri-snRNP into the spliceosome. (PMID: 18425142) Mathew R … Lührmann R (Nature structural & molecular biology 2008) 3 4 23
  3. The human U5-200kD DEXH-box protein unwinds U4/U6 RNA duplices in vitro. (PMID: 9539711) Laggerbauer B … Lührmann R (Proceedings of the National Academy of Sciences of the United States of America 1998) 2 3 23
  4. Transcription Dynamics Prevent RNA-Mediated Genomic Instability through SRPK2-Dependent DDX23 Phosphorylation. (PMID: 28076779) Sridhara SC … de Almeida SF (Cell reports 2017) 3 4
  5. Identification of Novel Proteins Co-Purifying with Cockayne Syndrome Group B (CSB) Reveals Potential Roles for CSB in RNA Metabolism and Chromatin Dynamics. (PMID: 26030138) Nicolai S … Proietti-De-Santis L (PloS one 2015) 3 4

Products for DDX23 Gene

  • Signalway Proteins for DDX23

Sources for DDX23 Gene